Well, if it helps anyone, this is my take on IT. It's not all a dream.
The oddity of the vision shift after Harbinger's beam is where I think the full on, no-holds-barred indoctrination attempt starts. Say, if Garrus was watching from the outside, he'd see Shepard fall to her knees as Harbinger's final attempt to stop her begins. Like... there was no beam. At least, not direct at Shepard, but Shepard thinks there was? And Garrus watches Shepard stumble toward the Crucible beam somehow still fighting (shooting Marauder Sheilds, etc). Can't get her attention, can't talk to her... nothing. All he can do is cover her back against the renewed onslaught of the reaper minions.
She gets up to the Citadel and the weirdness continues. She's actually walking forward. But like the dreams, with her deceased teammates' whispers, she's fighting it... bring in Anderson's hallucination. Harbinger counters with TIM. Shepard ends up shooting herself somewhere non-lethal and non-crippling to fight TIM. After all, pain will wake you from any dream, right? She sits down to rest, to quit, maybe give in to the urges to stop fighting -- she's hurting and wounded and tired, after all. And her mind counters with one more plea for help from Hackett.
The God Toddler exists, but it's on the Reapers' side. It wants the cycle to continue because then it continues. It's in a fight for self-preservation, too. Destroy and Synthesis break the Indoctrination (Sheps eyes glow green, not blue) (and I'm not certain about Synthesis). Control cements the indoctrination. In Control, in my head at least, Shep's body survives, but she's a tool of the Reapers and urges surrender because the Crucible didn't work.
The choices of Synthesis and Destroy, indoctrination is broken. I don't like Synthesis either because the Trekkie in me screams BORG! at the top of its lungs and reminds me that that will remove all free will, at least as we know it. But it's still not an ending the Reapers like because they lose.
I think the Reapers want the Crucible to be built. Especially if the God Toddler is on their side instead of the neutral party it tries to present itself as. I think it might magnify the Indoctrination signal to finally overwhelm Shepard. Which is what they've been trying to do all along. Hence the dreams.
Unlike the mainstream theory... I've never thought Shepard was indoctrinated since day 1, nor do I think the whole ending's a dream. I've thought that the Reapers have been attempting to indoctrinate her. But never actually succeeding, hence the warnings from her teammates in her dreams. If you listen to them, they all seem to be telling her to do other things than follow the child. Ashley's whisper in mine was the clearest, "Get the LT and get out of here!" And Mordin's "Implications, unpleasant," and "It had to be me, someone else would have gotten it wrong."